Assignment 5
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Assignment 5. Use the R annotation tools to investigate the top 20 genes in the Rice array experiment. Submit a gene list to David and see what you find. Try this with Gene Specific p-values < 0.05 Posterior p-values < 0.05 Posterior FDR p-values < 0.20

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Assignment 5

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Assignment 5

Assignment 5

  • Use the R annotation tools to investigate the top 20 genes in the Rice array experiment.

  • Submit a gene list to David and see what you find.

  • Try this with

    • Gene Specific p-values < 0.05

    • Posterior p-values < 0.05

    • Posterior FDR p-values < 0.20

  • Are there any qualitative differences? How many genes are in each of the three categories?

  • Can you figure out how to compute the overlap?


Assignment 5

> library(affy)

> rrdata<- ReadAffy()

> eset <- rma(rrdata)

> group <- factor(c(0,0,1,1,2,2,3,3,4,4,5,5))

> vlist <- list(group=group)

> eset.lmg <- neweS(exprs(eset),vlist)

> lmg.results <- LMGene(eset.lmg)

> pv1 <- genediff(eset.lmg)

> names(pv1)

[1] "Gene.Specific" "Posterior"

> pv2 <- pvadjust(genediff.results)

> names(pv2)

[1] "Gene.Specific" "Posterior" "Gene.Specific.FDR"

[4] "Posterior.FDR"

> sum(pv2$Gene.Specific < .05)

[1] 2615

> sum(pv2$Posterior < .05)

[1] 3082

> sum(pv2$Posterior.FDR < .20)

[1] 3360

SPH 247 Statistical Analysis of Laboratory Data


Assignment 5

> list1 <- pv1$Gene.Specific < .05

> list2 <- pv1$Posterior < .05

> list3 <- pv2$Posterior.FDR < .20

> gene.background<- featureNames(eset)

> sig.genes1 <- gene.background[list1]

> sig.genes2 <- gene.background[list2]

> sig.genes3 <- gene.background[list3]

> write(sig.genes1,"sig.genes1.txt")

> write(sig.genes2,"sig.genes2.txt")

> write(sig.genes3,"sig.genes3.txt")

> write(gene.background,"gene.background.txt")

> table(list1,list2,list3)

, , list3 = FALSE

list2

list1 FALSE TRUE

FALSE 8960 0

TRUE 305 0

, , list3 = TRUE

list2

list1 FALSE TRUE

FALSE 87 963

TRUE 16 2294[1] 1173


Assignment 5

GS < .05

2615

Posterior < .05

3082

305

0

0

2294

16

963

87

Posterior FDR < .20

3360

SPH 247 Statistical Analysis of Laboratory Data


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